Back to Rapid builds (Linux only) of a subset of BioC 3.22 Report updated every 6 hours |
This page was generated on 2025-08-23 09:59 -0400 (Sat, 23 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 916 |
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Package 188/229 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | |||||||
Rsubread 2.23.3 (landing page) Wei Shi
| teran2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||
To the developers/maintainers of the Rsubread package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: Rsubread |
Version: 2.23.3 |
Command: /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD check --install=check:Rsubread.install-out.txt --library=/home/rapidbuild/bbs-3.22-bioc-rapid/R/site-library --timings Rsubread_2.23.3.tar.gz |
StartedAt: 2025-08-23 09:10:07 -0400 (Sat, 23 Aug 2025) |
EndedAt: 2025-08-23 09:19:53 -0400 (Sat, 23 Aug 2025) |
EllapsedTime: 585.9 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: Rsubread.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD check --install=check:Rsubread.install-out.txt --library=/home/rapidbuild/bbs-3.22-bioc-rapid/R/site-library --timings Rsubread_2.23.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/meat/Rsubread.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * checking for file ‘Rsubread/DESCRIPTION’ ... OK * this is package ‘Rsubread’ version ‘2.23.3’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘Rsubread’ can be installed ... WARNING Found the following significant warnings: cell-counts.c:1134:47: warning: format ‘%d’ expects argument of type ‘int’, but argument 7 has type ‘int *’ [-Wformat=] cell-counts.c:3483:124: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘long int’ [-Wformat=] cell-counts.c:3788:19: warning: suggest parentheses around assignment used as truth value [-Wparentheses] cell-counts.c:4034:15: warning: suggest parentheses around assignment used as truth value [-Wparentheses] cell-counts.c:4120:15: warning: suggest parentheses around assignment used as truth value [-Wparentheses] cell-counts.c:4155:66: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘srInt_64’ {aka ‘long long int’} [-Wformat=] cell-counts.c:4155:71: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘long int’ [-Wformat=] cell-counts.c:4164:69: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘srInt_64’ {aka ‘long long int’} [-Wformat=] cell-counts.c:4164:74: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘long int’ [-Wformat=] cell-counts.c:5140:61: warning: format ‘%s’ expects argument of type ‘char *’, but argument 4 has type ‘void *’ [-Wformat=] cell-counts.c:5205:148: warning: format ‘%s’ expects argument of type ‘char *’, but argument 4 has type ‘void *’ [-Wformat=] cell-counts.c:5234:140: warning: format ‘%s’ expects argument of type ‘char *’, but argument 4 has type ‘void *’ [-Wformat=] cell-counts.c:6797:81: warning: format ‘%s’ expects argument of type ‘char *’, but argument 4 has type ‘void *’ [-Wformat=] cell-counts.c:2769:1: warning: control reaches end of non-void function [-Wreturn-type] cell-counts.c:3991:1: warning: control reaches end of non-void function [-Wreturn-type] See ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/meat/Rsubread.Rcheck/00install.out’ for details. * used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * checking installed package size ... INFO installed size is 39.8Mb sub-directories of 1Mb or more: annot 30.9Mb libs 4.0Mb qualf 3.4Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... WARNING Note: information on .o files is not available File ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rsubread/libs/Rsubread.so’: Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C) Found ‘stderr’, possibly from ‘stderr’ (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed align 20.097 27.000 47.173 propmapped 20.842 25.908 47.102 sublong 9.876 10.657 20.384 buildindex 3.807 3.542 7.751 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs See ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/meat/Rsubread.Rcheck/00check.log’ for details.
Rsubread.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD INSTALL Rsubread ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library’ * installing *source* package ‘Rsubread’ ... ** this is package ‘Rsubread’ version ‘2.23.3’ ** using staged installation @@@@@ The operating system is Linux. ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c HelperFunctions.c -o HelperFunctions.o In file included from HelperFunctions.c:56: subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp] 502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" | ^~~~~~~ gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c LRMbase-index.c -o LRMbase-index.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c LRMchro-event.c -o LRMchro-event.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c LRMfile-io.c -o LRMfile-io.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c LRMhashtable.c -o LRMhashtable.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c LRMhelper.c -o LRMhelper.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c LRMseek-zlib.c -o LRMseek-zlib.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c R_wrapper.c -o R_wrapper.o In file included from HelperFunctions.h:24, from R_wrapper.c:35: subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp] 502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" | ^~~~~~~ gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c RsimReads.c -o RsimReads.o In file included from RsimReads.c:21: subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp] 502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" | ^~~~~~~ gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c SNPCalling.c -o SNPCalling.o In file included from SNPCalling.c:33: subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp] 502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" | ^~~~~~~ gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c aligner.c -o aligner.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c atgcContent.c -o atgcContent.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c build-sam-index.c -o build-sam-index.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c cell-counts.c -o cell-counts.o In file included from cell-counts.c:13: subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp] 502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" | ^~~~~~~ cell-counts.c: In function ‘cellCounts_args_context’: cell-counts.c:721:2: warning: #warning "====== SHOULD REMOVE '* 4' BELOW =========" [-Wcpp] 721 | #warning "====== SHOULD REMOVE '* 4' BELOW =========" | ^~~~~~~ cell-counts.c:724:2: warning: #warning "====== SHOULD REMOVE '+ 4' BELOW =========" [-Wcpp] 724 | #warning "====== SHOULD REMOVE '+ 4' BELOW =========" | ^~~~~~~ cell-counts.c:816:26: warning: #warning "====== Yang Liao added '+20' for better junction calling -- think about it in final release??? ======" [-Wcpp] 816 | #warning "====== Yang Liao added '+20' for better junction calling -- think about it in final release??? ======" | ^~~~~~~ cell-counts.c: In function ‘cellCounts_write_one_chroEvent’: cell-counts.c:1134:47: warning: format ‘%d’ expects argument of type ‘int’, but argument 7 has type ‘int *’ [-Wformat=] 1134 | fprintf(wfp,"%s\t%d\t%d\t%s\t%d\n", chro, pos1, pos2, ce -> from_truth?"ANNOTATED":"NEW", ce -> step2_supported_reads); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int int * | %ls cell-counts.c: In function ‘cellCounts_copy_txn_to_juncs’: cell-counts.c:1287:1: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1287 | if(!ignore_GTF) cellCounts_add_or_update_chroEvent_in_table(cct_context, chroEvent_t_TYPE_EXON, chname_strand , start, end, 0, 1); | ^~ cell-counts.c:1289:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1289 | if(last_end>0){ | ^~ cell-counts.c:1267:28: warning: variable ‘last_start’ set but not used [-Wunused-but-set-variable] 1267 | int last_end = -1, last_start = -1; | ^~~~~~~~~~ cell-counts.c: In function ‘cellCounts_end_build_candidature_from_stacks’: cell-counts.c:3227:29: warning: unused variable ‘x_candidate’ [-Wunused-variable] 3227 | int x_3end, x_5end, x_candidate; | ^~~~~~~~~~~ cell-counts.c: In function ‘cellCounts_build_junction_read_finalise_current_stack’: cell-counts.c:3369:2: warning: #warning "========= THIS IS FOR TESTING EFFICIENCY; NOT NEEDED IN RELASED VERSIOn =============" [-Wcpp] 3369 | #warning "========= THIS IS FOR TESTING EFFICIENCY; NOT NEEDED IN RELASED VERSIOn =============" | ^~~~~~~ cell-counts.c: In function ‘cellCounts_tree_iterative_search’: cell-counts.c:3483:124: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘long int’ [-Wformat=] 3483 | if(0)if(strstr(thread_context -> realignment_event_read_name ,"R00000895964"))fprintf(stderr,"REMOTE_TEST TYPE %d LEN %d (%d) REMOTE_loc_read = %d TO3=%d %s\n", envdtl -> event_type, inslen, (void*)envdtl -> length - NULL, remote_first_matching_base_read, to3end, thread_context -> realignment_event_read_name); | ~^ | | | int | %ld cell-counts.c:3438:21: warning: unused variable ‘read_for_testing_len’ [-Wunused-variable] 3438 | int read_for_testing_len = edge_region_end - edge_region_start +1; | ^~~~~~~~~~~~~~~~~~~~ cell-counts.c: In function ‘cellCounts_add_covered_indels_in_table’: cell-counts.c:3788:19: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 3788 | for(x1=0; nch=result_cigar[x1] ; x1++){ | ^~~ cell-counts.c:3802:1: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 3802 | if(1) cellCounts_add_or_update_chroEvent_in_table(cct_context, chroEvent_t_TYPE_INDEL , chro_name, chro_pos -1, rposv, inslen_negative, 0); // thread safe | ^~ cell-counts.c:3803:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 3803 | if(nch=='D') chro_cursor += tmpi; | ^~ cell-counts.c: In function ‘cellCounts_call_juncs_put_in_tab’: cell-counts.c:3903:45: warning: variable ‘rgap’ set but not used [-Wunused-but-set-variable] 3903 | int rgap = -1; | ^~~~ cell-counts.c:3933:26: warning: #warning "==== Think: could a read contribute multiple junctions? could a major half contribute multiple junctions? ====" [-Wcpp] 3933 | #warning "==== Think: could a read contribute multiple junctions? could a major half contribute multiple junctions? ====" | ^~~~~~~ cell-counts.c:3943:37: warning: unused variable ‘manegative’ [-Wunused-variable] 3943 | int manegative = votetab -> masks[mai][maj]; | ^~~~~~~~~~ cell-counts.c:3855:29: warning: variable ‘best_GTAG_negative’ set but not used [-Wunused-but-set-variable] 3855 | int best_GTAG_negative = -1; | ^~~~~~~~~~~~~~~~~~ cell-counts.c:3823:38: warning: unused variable ‘distinct_vote_number_i’ [-Wunused-variable] 3823 | int i,j,reverse_text_offset, distinct_vote_number_i; | ^~~~~~~~~~~~~~~~~~~~~~ cell-counts.c:3823:17: warning: unused variable ‘reverse_text_offset’ [-Wunused-variable] 3823 | int i,j,reverse_text_offset, distinct_vote_number_i; | ^~~~~~~~~~~~~~~~~~~ cell-counts.c: In function ‘cellCounts_add_supported_unsupported_reads_from_cigar’: cell-counts.c:4034:15: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 4034 | while(nch = cigar[x1++]){ | ^~~ cell-counts.c:4096:66: warning: variable ‘x2_not_matter’ set but not used [-Wunused-but-set-variable] 4096 | int is_the_last, x2_not_matter; | ^~~~~~~~~~~~~ cell-counts.c:4120:15: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 4120 | while(nch = cigar[x1++]){ | ^~~ cell-counts.c:4130:81: warning: array subscript has type ‘char’ [-Wchar-subscripts] 4130 | IVT_IntervalTreeNode * myroot = LR_roots[LRi]; | ^ cell-counts.c:4155:66: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘srInt_64’ {aka ‘long long int’} [-Wformat=] 4155 | if(0)fprintf(stderr,"SUPP_NON query-cov %d ~ %d non-env-cov %d ~ %d %s\n", Mstart_base, Mlast_base, evb -> start, evb -> attr -NULL , is_the_last?"SKIPPED":"ADDED"); | ~^ ~~~~~~~~~~~~ | | | | int srInt_64 {aka long long int} | %lld cell-counts.c:4155:71: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘long int’ [-Wformat=] 4155 | if(0)fprintf(stderr,"SUPP_NON query-cov %d ~ %d non-env-cov %d ~ %d %s\n", Mstart_base, Mlast_base, evb -> start, evb -> attr -NULL , is_the_last?"SKIPPED":"ADDED"); | ~^ | | | int | %ld cell-counts.c:4164:69: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘srInt_64’ {aka ‘long long int’} [-Wformat=] 4164 | if(0)fprintf(stderr,"SUPP_X2TEST query-cov %d ~ %d non-env-cov %d ~ %d X2 %d %s\n", Mstart_base, Mlast_base, evb -> start, evb -> attr -NULL , x2, (is_the_last && is_same_x2)?"SKIPPED":"ADDED"); | ~^ ~~~~~~~~~~~~ | | | | int srInt_64 {aka long long int} | %lld cell-counts.c:4164:74: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘long int’ [-Wformat=] 4164 | if(0)fprintf(stderr,"SUPP_X2TEST query-cov %d ~ %d non-env-cov %d ~ %d X2 %d %s\n", Mstart_base, Mlast_base, evb -> start, evb -> attr -NULL , x2, (is_the_last && is_same_x2)?"SKIPPED":"ADDED"); | ~^ | | | int | %ld cell-counts.c:4022:41: warning: unused variable ‘x3’ [-Wunused-variable] 4022 | int nch, tmpi=0, x1=0, b1off=0, x3; | ^~ cell-counts.c: In function ‘cellCounts_do_one_batch_UMI_merge_one_cell’: cell-counts.c:5140:61: warning: format ‘%s’ expects argument of type ‘char *’, but argument 4 has type ‘void *’ [-Wformat=] 5140 | fprintf( cct_context -> read_assignment_detail_fp, "UMI_FINALLY_ASSIGN\tSAMPLE%03d\t%s\t%s\t%s\n",sample_no, ArrayListGet(cct_context -> cell_barcodes_array, bc), str1 -> umi, cct_context ->gene_name_array[gn]);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | void * cell-counts.c:5158:41: note: in expansion of macro ‘ADD_count_hash’ 5158 | ADD_count_hash(str1->cellbc, str1->gene_no,1); | ^~~~~~~~~~~~~~ cell-counts.c:5140:95: note: format string is defined here 5140 | fprintf( cct_context -> read_assignment_detail_fp, "UMI_FINALLY_ASSIGN\tSAMPLE%03d\t%s\t%s\t%s\n",sample_no, ArrayListGet(cct_context -> cell_barcodes_array, bc), str1 -> umi, cct_context ->gene_name_array[gn]);\ | ~^ | | | char * | %p cell-counts.c:5205:148: warning: format ‘%s’ expects argument of type ‘char *’, but argument 4 has type ‘void *’ [-Wformat=] 5205 | fprintf( cct_context -> read_assignment_detail_fp, "FIX_UMI_SIMILAR\tSAMPLE%03d\t%s\t%s\t%s\t%s\n",sample_no, ArrayListGet(cct_context -> cell_barcodes_array, acc_str -> cellbc), try_str -> umi, acc_str -> umi, cct_context ->gene_name_array[ acc_str -> gene_no ]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | char * void * | %p cell-counts.c:5234:140: warning: format ‘%s’ expects argument of type ‘char *’, but argument 4 has type ‘void *’ [-Wformat=] 5234 | fprintf( cct_context -> read_assignment_detail_fp, "FIX_UMI_SIMILAR\tSAMPLE%03d\t%s\t%s\t%s\t%s\n",sample_no, ArrayListGet(cct_context -> cell_barcodes_array, acc_str -> cellbc), try_str -> umi, acc_str -> umi, cct_context ->gene_name_array[ acc_str -> gene_no ]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | char * void * | %p cell-counts.c: In function ‘cellCounts_do_one_batch_UMI_merge_one_step’: cell-counts.c:5140:61: warning: format ‘%s’ expects argument of type ‘char *’, but argument 4 has type ‘void *’ [-Wformat=] 5140 | fprintf( cct_context -> read_assignment_detail_fp, "UMI_FINALLY_ASSIGN\tSAMPLE%03d\t%s\t%s\t%s\n",sample_no, ArrayListGet(cct_context -> cell_barcodes_array, bc), str1 -> umi, cct_context ->gene_name_array[gn]);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | void * cell-counts.c:5305:66: note: in expansion of macro ‘ADD_count_hash’ 5305 | else if(is_UMI_step2 && str1->cellbc>=0) ADD_count_hash(str1->cellbc,str1->gene_no,1); | ^~~~~~~~~~~~~~ cell-counts.c:5140:95: note: format string is defined here 5140 | fprintf( cct_context -> read_assignment_detail_fp, "UMI_FINALLY_ASSIGN\tSAMPLE%03d\t%s\t%s\t%s\n",sample_no, ArrayListGet(cct_context -> cell_barcodes_array, bc), str1 -> umi, cct_context ->gene_name_array[gn]);\ | ~^ | | | char * | %p cell-counts.c: In function ‘cellCounts_find_nearest_gene_dist’: cell-counts.c:6797:81: warning: format ‘%s’ expects argument of type ‘char *’, but argument 4 has type ‘void *’ [-Wformat=] 6797 | if(0)if( gene_name_list -> numOfElements )fprintf(stderr,"SUBADD_DIST of %lld, %s\n", gene_name_list -> numOfElements, gene_name_list -> elementList[0]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | char * void * | %p cell-counts.c: In function ‘cellCounts_write_final_junctions’: cell-counts.c:6921:21: warning: unused variable ‘unique_junctions’ [-Wunused-variable] 6921 | int unique_junctions = 0; | ^~~~~~~~~~~~~~~~ cell-counts.c:6902:20: warning: unused variable ‘ky_i2’ [-Wunused-variable] 6902 | int ky_i1, ky_i2; | ^~~~~ cell-counts.c:6902:13: warning: unused variable ‘ky_i1’ [-Wunused-variable] 6902 | int ky_i1, ky_i2; | ^~~~~ cell-counts.c:6900:81: warning: unused variable ‘gene_name_tail’ [-Wunused-variable] 6900 | char * gene_names = malloc(max_junction_genes * FEATURE_NAME_LENGTH), * gene_name_tail; | ^~~~~~~~~~~~~~ cell-counts.c:6869:13: warning: unused variable ‘infile_i’ [-Wunused-variable] 6869 | int infile_i, disk_is_full = 0; | ^~~~~~~~ cell-counts.c: In function ‘cellCounts_release_context_from_align’: cell-counts.c:2769:1: warning: control reaches end of non-void function [-Wreturn-type] 2769 | } | ^ cell-counts.c: In function ‘cellCounts_call_juncs_put_in_tab’: cell-counts.c:3991:1: warning: control reaches end of non-void function [-Wreturn-type] 3991 | } | ^ cell-counts.c: In function ‘cellCounts_find_hits_for_mapped_section’: cell-counts.c:2231:19: warning: ‘search_start’ may be used uninitialized [-Wmaybe-uninitialized] 2231 | if(search_start>0xffffff00) return; | ^ cell-counts.c:2220:30: note: ‘search_start’ was declared here 2220 | unsigned int search_start, search_end, search_block_id; | ^~~~~~~~~~~~ gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c core-bigtable.c -o core-bigtable.o In file included from core.h:46, from core-bigtable.c:12: subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp] 502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" | ^~~~~~~ gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c core-indel.c -o core-indel.o In file included from HelperFunctions.h:24, from core-indel.c:28: subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp] 502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" | ^~~~~~~ gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c core-interface-aligner.c -o core-interface-aligner.o In file included from core-interface-aligner.c:7: subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp] 502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" | ^~~~~~~ gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c core-interface-subjunc.c -o core-interface-subjunc.o In file included from core-interface-subjunc.c:7: subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp] 502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" | ^~~~~~~ gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c core-junction.c -o core-junction.o In file included from core-junction.c:25: subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp] 502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" | ^~~~~~~ core-junction.c: In function ‘find_donor_receptor’: core-junction.c:2099:25: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2099 | if(0&& FIXLENstrcmp("V0112_0155:7:1101:12618:2466#ACTTGA", rname) == 0) | ^~ core-junction.c:2103:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2103 | if( (end_site_mismatches + start_site_mismatches) * 500 + insertion_in_between_i < best_testing_score ){ | ^~ gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c core.c -o core.o In file included from core.c:45: subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp] 502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" | ^~~~~~~ gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c detection-calls.c -o detection-calls.o In file included from detection-calls.c:8: subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp] 502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" | ^~~~~~~ detection-calls.c: In function ‘DTCwrite_annotations’: detection-calls.c:155:9: warning: dangling pointer ‘gc_2int’ to an unnamed temporary may be used [-Wdangling-pointer=] 155 | DTCadd_annotation(context, gene_name, chro_name, start, end, is_negative_strand, gc_2int[0], gc_2int[1], 0); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ detection-calls.c:154:48: note: unnamed temporary defined here 154 | if(!gc_2int) gc_2int = (unsigned int[]){0,0,0}; | ^ detection-calls.c:155:109: warning: dangling pointer ‘gc_2int’ to an unnamed temporary may be used [-Wdangling-pointer=] 155 | DTCadd_annotation(context, gene_name, chro_name, start, end, is_negative_strand, gc_2int[0], gc_2int[1], 0); | ^ detection-calls.c:154:48: note: unnamed temporary defined here 154 | if(!gc_2int) gc_2int = (unsigned int[]){0,0,0}; | ^ detection-calls.c:155:9: warning: dangling pointer ‘gc_2int’ to an unnamed temporary may be used [-Wdangling-pointer=] 155 | DTCadd_annotation(context, gene_name, chro_name, start, end, is_negative_strand, gc_2int[0], gc_2int[1], 0); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ detection-calls.c:154:48: note: unnamed temporary defined here 154 | if(!gc_2int) gc_2int = (unsigned int[]){0,0,0}; | ^ gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c detectionCall.c -o detectionCall.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c detectionCallAnnotation.c -o detectionCallAnnotation.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c exon-algorithms.c -o exon-algorithms.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c exon-align-indel.c -o exon-align-indel.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c exon-align.c -o exon-align.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c flattenAnnotations.c -o flattenAnnotations.o In file included from flattenAnnotations.c:41: subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp] 502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" | ^~~~~~~ gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c fullscan.c -o fullscan.o In file included from fullscan.c:26: subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp] 502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" | ^~~~~~~ gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c fusion-align.c -o fusion-align.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c gen_rand_reads.c -o gen_rand_reads.o In file included from gen_rand_reads.c:26: subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp] 502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" | ^~~~~~~ gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c gene-algorithms.c -o gene-algorithms.o In file included from gene-algorithms.c:36: subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp] 502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" | ^~~~~~~ gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c gene-value-index.c -o gene-value-index.o In file included from gene-value-index.h:24, from gene-value-index.c:25: subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp] 502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" | ^~~~~~~ gene-value-index.c: In function ‘is_offset_in_chro’: gene-value-index.c:85:33: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 85 | if( pos < chros -> padding || pos >= ( chros->read_offsets[n] - chros->read_offsets[n-1] - chros -> padding )) | ^~ subread.h:153:24: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 153 | #define SUBREADprintf msgqu_printf | ^~~~~~~~~~~~ gene-value-index.c:87:41: note: in expansion of macro ‘SUBREADprintf’ 87 | SUBREADprintf("INCHRO:%d ; POS:%d\n", ret, pos); | ^~~~~~~~~~~~~ gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c hashtable.c -o hashtable.o In file included from core.h:46, from hashtable.c:18: subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp] 502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" | ^~~~~~~ gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c index-builder.c -o index-builder.o In file included from gene-value-index.h:24, from index-builder.c:31: subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp] 502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" | ^~~~~~~ gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c input-blc.c -o input-blc.o In file included from input-blc.c:8: subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp] 502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" | ^~~~~~~ input-blc.c: In function ‘iCache_continuous_read_lanes’: input-blc.c:580:59: warning: unused variable ‘npos’ [-Wunused-variable] 580 | long long npos = lseek(tfp -> cbcl_bin_fd, next_tile_start_off , SEEK_SET); | ^~~~ gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c input-files.c -o input-files.o In file included from input-files.h:23, from input-files.c:35: subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp] 502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" | ^~~~~~~ input-files.c: In function ‘reduce_SAM_to_BAM’: input-files.c:3244:13: warning: unused variable ‘seq_len’ [-Wunused-variable] 3244 | int seq_len = qual - seq - 1; | ^~~~~~~ input-files.c: In function ‘SAM_pairer_fix_format’: input-files.c:4863:50: warning: variable ‘readname’ set but not used [-Wunused-but-set-variable] 4863 | char tmpfname [MAX_FILE_NAME_LENGTH+14], readname[256]; | ^~~~~~~~ gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c interval_merge.c -o interval_merge.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c long-hashtable.c -o long-hashtable.o In file included from core.h:46, from long-hashtable.c:31: subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp] 502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" | ^~~~~~~ gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c longread-mapping.c -o longread-mapping.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c mergeVCF.c -o mergeVCF.o In file included from mergeVCF.c:7: subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp] 502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" | ^~~~~~~ gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c processExons.c -o processExons.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c propmapped.c -o propmapped.o In file included from propmapped.c:34: subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp] 502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" | ^~~~~~~ gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c qualityScores.c -o qualityScores.o In file included from qualityScores.c:27: subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp] 502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" | ^~~~~~~ gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c read-repair.c -o read-repair.o In file included from read-repair.c:6: subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp] 502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" | ^~~~~~~ gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c readSummary.c -o readSummary.o In file included from readSummary.c:41: subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp] 502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" | ^~~~~~~ readSummary.c: In function ‘vote_and_add_count’: readSummary.c:3900:58: warning: variable ‘assignment_target_number’ set but not used [-Wunused-but-set-variable] 3900 | srInt_64 assignment_target_number = tmp_voter_id; | ^~~~~~~~~~~~~~~~~~~~~~~~ readSummary.c: In function ‘fc_thread_merge_results’: readSummary.c:3970:32: warning: unused variable ‘sample_i’ [-Wunused-variable] 3970 | int xk1, xk2, ret = 0, sample_i; | ^~~~~~~~ readSummary.c: In function ‘fc_write_final_junctions’: readSummary.c:5724:21: warning: unused variable ‘unique_junctions’ [-Wunused-variable] 5724 | int unique_junctions = 0; | ^~~~~~~~~~~~~~~~ readSummary.c:5700:20: warning: unused variable ‘ky_i2’ [-Wunused-variable] 5700 | int ky_i1, ky_i2; | ^~~~~ readSummary.c:5700:13: warning: unused variable ‘ky_i1’ [-Wunused-variable] 5700 | int ky_i1, ky_i2; | ^~~~~ readSummary.c:5698:81: warning: unused variable ‘gene_name_tail’ [-Wunused-variable] 5698 | char * gene_names = malloc(max_junction_genes * FEATURE_NAME_LENGTH), * gene_name_tail; | ^~~~~~~~~~~~~~ readSummary.c: In function ‘readSummary’: readSummary.c:5971:52: warning: variable ‘scrna_total_BAM_no’ set but not used [-Wunused-but-set-variable] 5971 | int isGTF, n_input_files=0,is_dual_index, scrna_total_BAM_no; | ^~~~~~~~~~~~~~~~~~ readSummary.c: In function ‘vote_and_add_count’: readSummary.c:3833:66: warning: ‘longest_overlap_score’ may be used uninitialized [-Wmaybe-uninitialized] 3833 | if(longest_overlap_score > scoring_numbers[score_x1]) scoring_numbers[score_x1] = 0; | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ readSummary.c:3602:51: note: ‘longest_overlap_score’ was declared here 3602 | int scoring_count = 0, score_x1, longest_overlap_score; | ^~~~~~~~~~~~~~~~~~~~~ gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c removeDupReads.c -o removeDupReads.o In file included from removeDupReads.c:27: subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp] 502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" | ^~~~~~~ gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c sam2bed.c -o sam2bed.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c sambam-file.c -o sambam-file.o In file included from sambam-file.c:33: subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp] 502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" | ^~~~~~~ gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c seek-zlib.c -o seek-zlib.o In file included from core.h:46, from seek-zlib.c:2: subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp] 502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" | ^~~~~~~ gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c sorted-hashtable.c -o sorted-hashtable.o In file included from sorted-hashtable.h:25, from sorted-hashtable.c:20: subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp] 502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" | ^~~~~~~ gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c sublog.c -o sublog.o In file included from sublog.c:26: subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp] 502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" | ^~~~~~~ gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c tx-unique.c -o tx-unique.o In file included from tx-unique.h:4, from tx-unique.c:6: subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp] 502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" | ^~~~~~~ gcc -std=gnu2x -shared -L/usr/local/lib -o Rsubread.so HelperFunctions.o LRMbase-index.o LRMchro-event.o LRMfile-io.o LRMhashtable.o LRMhelper.o LRMseek-zlib.o LRMsorted-hashtable.o R_wrapper.o RsimReads.o SNPCalling.o aligner.o atgcContent.o build-sam-index.o cell-counts.o core-bigtable.o core-indel.o core-interface-aligner.o core-interface-subjunc.o core-junction.o core.o detection-calls.o detectionCall.o detectionCallAnnotation.o exon-algorithms.o exon-align-indel.o exon-align.o flattenAnnotations.o fullscan.o fusion-align.o gen_rand_reads.o gene-algorithms.o gene-value-index.o hashtable.o index-builder.o input-blc.o input-files.o interval_merge.o long-hashtable.o longread-mapping.o mergeVCF.o processExons.o propmapped.o qualityScores.o read-repair.o readSummary.o removeDupReads.o sam2bed.o sambam-file.o seek-zlib.o sorted-hashtable.o sublog.o tx-unique.o -lz -lpthread -DMAKE_FOR_EXON installing to /media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/00LOCK-Rsubread/00new/Rsubread/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Rsubread)
Rsubread.Rcheck/Rsubread-Ex.timings
name | user | system | elapsed | |
align | 20.097 | 27.000 | 47.173 | |
buildindex | 3.807 | 3.542 | 7.751 | |
cellCounts | 0 | 0 | 0 | |
featureCounts | 0.001 | 0.000 | 0.000 | |
findCommonVariants | 0 | 0 | 0 | |
getInBuiltAnnotation | 0.194 | 0.031 | 0.231 | |
promoterRegions | 0.976 | 0.012 | 0.990 | |
propmapped | 20.842 | 25.908 | 47.102 | |
qualityScores | 0.024 | 0.001 | 0.025 | |
simReads | 0 | 0 | 0 | |
sublong | 9.876 | 10.657 | 20.384 | |